You're not risking grief or damage to the electronics or your speakers with your current setup.

It's just that you're running the audio signals through two preamp sections and two volume controls, because the PM16 is not a basic power amplifier and lacks power-amp inputs. It makes for a somewhat convoluted setup, with two volume controls to adjust when there should only be one.

Try it with out the PM 16(with out Audyssey but level matched) and then try it with the PM 16(with out Audyssey and level matched) and then have fun trying to decide which way it sounds better if there is any difference. If you don't hear a difference then you might as well make things easy and leave the PM-16 out of it.

Jasper, "grief" wasn't described, but as Alan pointed out, the theoretical objection is that the sound runs through two preamp sections rather than one, adding a small amount of extra distortion. This is unlikely to be audible, and if you like to use the PM16, carry on.

If the main speaker level trim was set in the 6004 to the minimum -12dB available(possibly indicating a lower setting was wanted)during calibration, lower the PM16 volume control a bit so that the calibration number comes out higher.

Edit: Roy, once the level is properly calibrated, the PM16 level control wouldn't have to be changed; any volume changes would be done in the 6004.